You COULD put on the PI heads on the pre-99 engines, but youd have a higher compression ratio and would have to use the 99 and later intake manifold. The pre 99 engines had flat top pistons and larger comb. chambers, and 99 and laters have dished pistons and smaller combustion chambers. You add PI heads to flat top pistons and you get a big compression ratio.

Although you might run into small problems such as EGR fitment and dipstick location and what not, the parts will all still fit with each other...given you use the same kind of intake as the heads. Its much the same as building a 302 and trying to decide which water pump to use, or serpentine or v-belt. They all fit, its just a matter of matching your parts correctly.

True, its not as perfect as it sounded on paper, but even ford says the modular engine family was created "so they could share similar production tooling and have many interchangeable parts."